In Nature Biotechnology this week, researchers from Stanford University and Illumina publish details of a method for whole-genome haplotyping using a statistical algorithm to take advantage of the partially phased information contained in long genomic fragments analyzed by short-read sequencing. For a human sample, they report that as little as 30 gigabase pairs of additional sequencing data are needed to phase genotypes identified by 50x coverage whole-genome sequencing, and the team used the method to phase 99 percent of single-nucleotide variants in three human genomes into long haplotype blocks between 0.2 megabase pairs and 1 megabase pairs in length. "Our analysis yielded a base-resolution map of DNA methylation across a human genome, which is a valuable resource for understanding mechanisms involving allele-specific DNA methylation," they add.
Meanwhile, in Nature Genetics, an international group of researchers report on a high-resolution taxonomic and protein functional characterization of the ancient oral microbiome using calcified dental plaque from medieval adult human skeletons. The investigators characterized the ancient oral microbiome in a diseased state and found 40 opportunistic pathogens; ancient human-associated putative antibiotic-resistance genes; a genome reconstruction of the periodontal pathogen Tannerella forsythia; 239 bacterial and 43 human proteins; and DNA sequences matching dietary sources.
Daily Scan has a bit more on this study here.